This issue occurs with Lync 2010 client as well as Skype 2013 client.
When a user logs onto a computer and lync tries to pass through credentials it fails and prompts for credentials.
Under the username section you have to remove the email address and enter \username and then it works fine.
We have about 12,000 clients and we get 6-10 calls per day.
Any help would be appreciated.